This is a legacy script for counting nanoparticles on optical fibers from SEM
images used at GWU. It is being supplanted by the AuNPModel script in pyparty_.
It is unlikely that the entire script will be migrated; however, because there's
just too much nuance to start mucking with. What I probably will change is IO
and CONFIG to make it more accessible, as well as possible change the thresholding
style if there's time for that.
.. _pyparty : https://github.com/hugadams/pyparty
Checkout out RunResults folder to see if the types of output is useful for your project. If
This is our ad-hoc workflow that this script inentionally was built for. It assumes a very particular directory structure, in particular that folders arranged by magnificaiton
Root ---> 50000 ----> Image1, Image2 etc...
A walker goes from image to image and does the following:
- Threshold and segment via ImageJ (SHOULD WITH SCIKIT IMAGE)
- Store particle data in pandas dataframe (SHOULD BE REPLACED BY PYPARTY)
- Bin particles, fit a guassian to histogram and segment AuNPs based on size considerations.
- Extrapolate the number of particles on the full fiber surface.
- Estimate the number of BSA based on a shell filling model.
You can always ask me directly to help analyze your images if for whatever reason, this script is useful to you. [email protected]
I'm a PhD student at GWU (check me out on researchgate_ and Linkedin_) and former Enthought intern. I work in biomolecule sensing and nanophotonics.
.. _researchgate : https://www.researchgate.net/profile/Adam_Hughes2/?ev=hdr_xprf .. _Linkedin : http://www.linkedin.com/profile/view?id=121484744&goback=%2Enmp_*1_*1_*1_*1_*1_*1_*1_*1_*1_*1_*1&trk=spm_pic